[gmx-users] doubts on g_confrms output

[Mark Abraham]

On 12/02/2011 2:55 AM, Kwee Hong wrote:
> Hi Tsjerk,
>
> Thanks for the help. I got it.
> But do you have any idea how to solve this in vmd?

Use trjconv -sep on the .pdb file to split it.

Mark

>
> Regards,
> Joyce
>
> ------------------------------------------------------------------------
> *From:* Tsjerk Wassenaar <tsjerkw at gmail.com>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Saturday, January 22, 2011 15:53:22
> *Subject:* Re: [gmx-users] doubts on g_confrms output
>
> Hi Joyce,
>
> In pymol use 'set all_states'
>
> Cheers,
>
> Tsjerk
>
>> On Jan 22, 2011 8:30 AM, "Kwee Hong" <jestan1985 at yahoo.com 
>> <mailto:jestan1985 at yahoo.com>> wrote:
>>
>> Hi,
>>
>> I was trying to do some analysis following John's "GROMACS tutorial 
>> for solvation study of spider toxin peptide".
>> I'm using GROMACS-4.5.3 and my command line for g_confrms is
>>
>> g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb
>>
>> The program calculated the RMSD sucessfully and fit_wet.pdb was 
>> generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the 
>> structure is obviously in a mess. And when I tried it out with pymol, 
>> I can only visualised one model. Model 2 did not appear. I wonder 
>> would it be the pdb format generated by g_confrms is not the standard 
>> pdb format and had caused VMD and final failed to read them?
>>
>> Herein, I attached part of the pdb file generated by fit_wet.pdb. Any 
>> insight is welcomed.
>>
>> Thanks,
>> Joyce
>>
>>
>>
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